A JSON-LD document with a top-level `@id` *and* `@graph` places its terms in a named
graph. `rdflib.Graph.parse()` loads only the default graph and discards the rest
without raising, so every class and property in such a document was dropped while
the load reported success.
`OntologyIngestor.ingest_ontology` now parses into a `Dataset` and flattens the
quads into the working `Graph`, keeping both the default and the named graphs. This
is the same `Graph` -> `Dataset` migration #757 made for `JenaStore` (#756); the
ingest path was not covered by it.
Measured on the 12-line reproduction from the issue:
before classes=0 properties=0
after classes=2 properties=0
On a real ontology the gap is larger: 25 triples / 1 subject against 719 / 88 for
the document that surfaced this.
Tests: `tests/ingest/test_ontology_named_graph.py` covers the named-graph document,
keeps a canary on the default-graph document so the fix cannot trade one blind spot
for another, and asserts that the reported result matches the terms returned.
Reverting `Dataset()` to `Graph()` turns all four red.
`tests/ontology`, `tests/export` and `tests/ingest` pass apart from six failures in
web/feed/database/API ingestion, unrelated to this change and failing the same way
on an unmodified checkout.
Not included, and happy to add here or as a follow-up: making a load that yields
zero classes stop returning `status: "success"`. That value is what made this take
an afternoon to find, but it is a behaviour change on a different layer and seemed
worth reviewing on its own.
